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This page was generated on 2022-01-20 11:05:53 -0500 (Thu, 20 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4162
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4057
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3999
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4116
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for karyoploteR on nebbiolo1


To the developers/maintainers of the karyoploteR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/karyoploteR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 973/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
karyoploteR 1.21.3  (landing page)
Bernat Gel
Snapshot Date: 2022-01-19 13:55:26 -0500 (Wed, 19 Jan 2022)
git_url: https://git.bioconductor.org/packages/karyoploteR
git_branch: master
git_last_commit: 6fc3dfd
git_last_commit_date: 2022-01-19 05:33:07 -0500 (Wed, 19 Jan 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  YES
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'regioneR' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

Summary

Package: karyoploteR
Version: 1.21.3
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings karyoploteR_1.21.3.tar.gz
StartedAt: 2022-01-19 19:42:43 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 19:49:32 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 408.4 seconds
RetCode: 0
Status:   OK  
CheckDir: karyoploteR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings karyoploteR_1.21.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/karyoploteR.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.21.3’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘karyoploteR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘regioneR’ ‘GenomicRanges’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
kpPlotDensity     30.790  5.072  35.865
kpPlotGenes       18.833  0.196  19.030
mergeTranscripts  13.184  0.090  13.274
kpPlotHorizon     12.815  0.032  12.848
kpPlotRegions     10.743  0.060  10.803
kpPlotBAMCoverage  7.275  1.184   8.461
kpPlotTranscripts  5.057  0.008   5.064
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.



Installation output

karyoploteR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL karyoploteR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘karyoploteR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (karyoploteR)

Tests output

karyoploteR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(karyoploteR)
Loading required package: regioneR
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> test_check("karyoploteR")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 181 ]
> 
> proc.time()
   user  system elapsed 
 14.603   0.698  15.290 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames1.7880.0561.844
autotrack0.0000.0010.001
colByCategory0.0020.0000.003
colByChr0.4510.0040.454
colByRegion1.0650.1281.193
colByValue0.2030.0000.203
darker0.0010.0000.001
filterParams0.0000.0000.001
findIntersections0.1120.0000.113
getChromosomeNamesBoundingBox0.0460.0160.061
getColorSchemas0.0010.0040.004
getCytobandColors0.0000.0020.002
getCytobands0.0000.0010.002
getDataPanelBoundingBox0.0370.0040.042
getDefaultPlotParams0.0670.0080.075
getMainTitleBoundingBox0.0330.0000.033
getTextSize0.0770.0040.082
getVariantsColors0.0010.0000.001
horizonColors0.0040.0000.004
is.color0.0010.0000.001
kpAbline1.8930.1602.055
kpAddBaseNumbers0.3170.0000.317
kpAddChromosomeNames0.0320.0000.031
kpAddChromosomeSeparators0.4200.0270.448
kpAddColorRect0.1760.0580.234
kpAddCytobandLabels0.3350.0000.335
kpAddCytobands0.0290.0000.029
kpAddCytobandsAsLine0.0660.0030.070
kpAddLabels0.4350.0080.444
kpAddMainTitle0.0310.0000.031
kpArea0.3250.0000.325
kpArrows0.5200.0040.524
kpAxis0.300.020.32
kpBars0.2010.0000.201
kpDataBackground0.2060.0000.206
kpHeatmap0.1300.0000.131
kpLines0.2470.0000.247
kpPlotBAMCoverage7.2751.1848.461
kpPlotBAMDensity1.8270.0281.855
kpPlotBigWig0.8330.1000.934
kpPlotCoverage0.3680.0280.396
kpPlotDensity30.790 5.07235.865
kpPlotGenes18.833 0.19619.030
kpPlotHorizon12.815 0.03212.848
kpPlotLinks0.860.000.86
kpPlotLoess0.0560.0000.057
kpPlotManhattan4.8840.0324.916
kpPlotMarkers1.4210.0081.429
kpPlotNames0.1050.0000.106
kpPlotRainfall0.6450.0040.649
kpPlotRegions10.743 0.06010.803
kpPlotRibbon0.0720.0000.072
kpPlotTranscripts5.0570.0085.064
kpPoints0.2030.0040.207
kpPolygon0.2100.0040.214
kpRect0.560.000.56
kpSegments0.4060.0000.406
kpText0.2330.0000.233
lighter0.0010.0000.001
makeGenesDataFromTxDb2.6070.0152.623
mergeTranscripts13.184 0.09013.274
plotDefaultPlotParams0.1260.0000.126
plotKaryotype0.8230.0080.830
plotPalettes0.0180.0000.018
prepareParameters20.0270.0000.027
prepareParameters40.0280.0000.029
processClipping0.030.000.03
transparent0.0000.0000.001